Professor Vardis Ntoukakis

Supervisor Details

Contact Details

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

Unlike animals, plants cannot move away from adverse conditions. Plants face increased threats from fungal and bacterial pathogens, some of which are gaining advantage as the climate becomes more favourable to them. To protect crops from major losses we need to understand how plants defend themselves and how we can exploit this.

Our laboratory addresses the important question of how plants respond to pathogen attack. This research will inform us as to where molecular biology and breeding approaches could be directed to optimise the existing cellular machinery to boost crop plant resistance to pathogens.

The lab uses both model and crop (tomato, brassica) plants to understand how pathogens are recognised and how plant immunity is supressed by pathogens.

We combine genome-wide approaches such as mRNA-seq, ChIP-seq, ATAC-seq and MNase-seq with proteomics, advance imaging, and biochemistry to enhance our understanding of how activation of Pattern Recognition Receptors (PRRs) and Resistance (R) proteins leads to plant immunity.

This research informs our efforts to engineering crop plants with durable resistance and increased crop yields.

Research Groups

Plant and Agricultural Biosciences

Quantitative, Systems and Engineering Biology

Warwick Integrative Synthetic Biology Centre (WISB)

MIBTP Project Details

Current Projects (2025-26)

Epigenetic regulation of plant immunity

Epigenetic Regulation of Plant Immunity

Secondary Supervisor(s): Professor Miriam Gifford

University of Registration: University of Warwick

BBSRC Strategic Research Priority:

Sustainable Agriculture and Food (Plant and Crop Science)
Understanding the Rules of Life (Plant Science)

Project Outline

Activation of plant immunity has to be finely balanced with other vital biological processes such as development and growth. A major part of plant immune responses is reprogramming of gene expression. During infection, plants are faced with the challenge of quickly changing their state of gene transcription by prioritizing defence responses over growth-related cellular functions. In all eukaryotic organisms the genomic DNA is packed into chromatin providing at the same time a barrier for transcription and an opportunity to regulate rapid changes in gene expression. A major mechanism controlling changes in chromatin structure and subsequently the partial/differential expression of the genome is localized chromatin remodelling.

Our laboratory has recently demonstrated that chromatin remodelling is a major mechanism controlling plant immunity^1,2,3.

The aim of this PhD project is to investigate the role of chromatin remodelling and epigenetics in the interplay between immunity and growth.

Histone-modifying enzymes add or remove covalent histone modifications that alter the accessibility of DNA to transcription factors, mediating the dynamic transition between expressed and repressed genomic regions. Histone acetylation is mediated by histone acetyltransferases(HATs) and deacetylases (HDACs), which deposit and remove acetyl groups from histones. The addition of acetyl groups on the N-terminus tails of histones reduce the affinity between histones and DNA, allowing the recruitment of the transcriptional machinery. Our laboratory has recently show that HATs regulate leaf immunity¹ and inheritable resistance against root pathogens². The aim of this project is to elucidate how HATs and HDACs regulate plant immunity against leaf and root pathogens.

1. Kim S., Piquerez S.J.M., Ramirez-Prado J.S., Mastorakis E., Veluchamy A., Latrasse D., Manza-Mianza D., Brik-Chaouche R., Huang Y, Rodriguez-Granados N.Y., Concia L., Blein T., Citerne S., Bendahmane A., Bergounioux C., Crespi M., Mahfouz M.M., Raynaud C., Hirt H., Benhamed M. Ntoukakis V. (2020) GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res., 48, (11), 5953-5966.

2.Gkizi D., González A.G., Pardal A. J., Piquerez S.J.M., Sergaki C., Tjamos S.E., Ntoukakis V. (2021) The bacterial biocontrol agent Paenibacillus alvei K165 confers inherited resistance against Verticillium dahliae. J. Exp. Bot. 72 (12), 4565-4576

3. Pardal A. J., Piquerez S.J.M., Dominguez-Ferreras A., Frungillo L., Mastorakis E., Reilly E., Latrasse D., Concia L., Gimenez-Ibanez S., Spoel S.H., Benhamed M., Ntoukakis V. (2020) Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLos Pathogens, 17 (5), e1009572

Techniques

The successful students will use cutting edge techniques including RNA-seq, ChIP-seq, MNase-seq and ATAC-seq together with statistical analysis and modelling to gain insight into the interplay between immunity and growth. After the initial characterisation using Arabidopsis thaliana plants, we will expand our investigation to tomato and brassica plants using CRISPR/Cas9 gene editing.

Unravelling the Regulatory Mechanisms of Effector-Triggered Immunity for Durable Plant Resistance

Secondary Supervisor(s): Professor Murray Grant

University of Registration: University of Warwick

BBSRC Strategic Research Priority:

Sustainable Agriculture and Food (Plant and Crop Science)
Understanding the Rules of Life (Plant Science)

Project Outline

Plant immunity heavily relies on R proteins capable of recognising pathogens and activating immunity. Yet this resistance often breaks under field conditions. Using the tomato-resistant protein Prf, this project aims to get a better understanding of the signalling cascades activated downstream pathogen recognition, with the aim of engineering plants with durable resistance.

Plant immunity largely depends on nucleotide-binding leucine-rich repeat (NLR) immune receptors, also known as resistance (R) proteins. These receptors detect pathogen-derived effectors and trigger effector-triggered immunity (ETI), a potent and highly effective defence mechanism.

Recent research using the tomato NLR Prf and its associated kinase Pto has revealed that mitogen-activated protein kinases (MAPKs) and helper NLRs called NRCs (NLR-required for cell death) associate with distinct parts of the Prf/Pto complex and are vital for the signalling processes that follow effector recognition. Additionally, the dissociation of the Prf/Pto complex into distinct modules upon effector recognition underpins a complex regulatory mechanism that governs the two downstream signalling pathways, MAPK activation and the formation of NRC oligomeric complexes, termed resistosomes, forming calcium-permeable cation channels at cellular membranes. These two signalling pathways converge in activation of immunity and cell death formation.

The proposed research aims to elucidate the molecular dynamics of the tomato Prf/Pto complex in response to pathogen effectors and to identify how different components of this complex regulate ETI signalling in tomatoes. Specifically, the research will focus on:

Investigating the timing and the mechanism underpinning the activation of MAPKs and NRCs.
Understanding the cross talk between MAPKs and NRCs, the two signalling pathways initiated by the activation of the resistance complex.
Exploring the dissociation dynamics of the Prf/Pto complex and its implications for the bifurcation of ETI signalling to engineer plants with durable resistance.

References

A. H. Sheikh, I. Zacharia, N. Tabassum, H. Virt, V. Ntoukakis, 14-3-3 proteins as a major hub for plant immunity. Trends Plant Sci, (2024).
A. H. Sheikh, I. Zacharia, A. J. Pardal, A. Dominguez-Ferreras, D. J. Sueldo, J. G. Kim, A. Balmuth, J. R. Gutierrez, B. F. Conlan, N. Ullah, O. M. Nippe, A. M. Girija, C. H. Wu, G. Sessa, A. M. E Jones, M. R. Grant, M. L. Gifford, M. B. Mudgett, J. P. Rathjen, V. Ntoukakis, Dynamic changes of the Prf/Pto tomato resistance complex following effector recognition. Nat Commun 14, 2568 (2023).
V. Ntoukakis, I. M. Saur, B. Conland, J. P. Rathjen, The changing of the guard: the Pto/Prf receptor complex of tomato and pathogen recognition. Curr Opin Plant Biol 20, 69-74 (2014).
V. Ntoukakis, T. S. Mucyn, S. Gimenez-Ibanez, H. C. Chapman, J. R. Gutierrez, A. L. Balmuth, A. M. Jones, J. P. Rathjen, Host inhibition of a bacterial virulence effector triggers immunity to infection. Science 324, 784-787 (2009).

Techniques

The student will gain expertise in protein biochemistry, molecular biology, proteomics, bioinformatics and advanced imaging techniques. The student will also apply synthetic biology approaches including gene editing to engineer plants with durable resistance.

Co-supervisor on projects with Professor Alex Jones and Professor Murray Grant.

Previous Projects (2024-25)

Co-supervisor on projects with Professor Murray Grant.

Previous Projects (2023-24)

Primary supervisor for:

Engineering Plants Tolerant to High Temperatures